My two cents:
I play 4-3/ Nickel and 100% Wishbone and just won a NC with it at 1-AA (1-A is still a freaking mystery given the elites set up). I have learned that unlike the great HarrisWb, this game favor passing over running. However, balance is generally the key.
I spend 20 min on each D and O PLUS 20 min on ST. Why? Because ST are 1/3 of the game. I also throw out of the wishbone about 40-50% of the time. Since I rarely throw to my TE (who blocks and provides more time for my QB), I will throw a lot to my 3 RBs.
As for Game planning, I am fairly simple. 0 to 3 yards is short, 3 to 10 is medium, 11 and up is long.
I know folks around here will tell you that fatigue doesn't matter, I think it does. I rotate players at 95%, which means I play a lot of players (good for development), but that single stud RB you currently have is only going to get 10-15 carries a game. Before the howlers come out, yes I know you can set it to 100% RB 1, but that's not the point.
If I am playing the high powered offense of thegruntboy for example who throws 99% of the time, I will use nickel 100% and then change the setting of one of my LBs to either make a 5-1-5 formation for short yardage (and then choose to rush 4 or 5) or the more standard, rush 4 and cover 7. The inverse is true if I were playing a 100% running team. I would run my 4-3 set and "walk an LB or two" to the line and have a standard 6-1-4 formation with one of them blitzing. In that scenario, my FASTEST OLB plays MLB and my MLB's are walked up.
The key is FORMATION building and usage. I have EIGHT different wishbone formations that I use on my game plan. Example, All run, blowout, 3 out (FB and TE block), 4 out, 5 out, 5 out long, etc....then you fit the personnel and the situation (down/distance, etc) to the plan. My FR QB generally plays under the 100% run playbook. My more experienced QBs will play in the run/pass portion.
Oh yeah and one other thing. RECRUIT well. It doesn't matter if you are Vince Lombardi, any amount of game planning is not going to help if the roster sucks(unless you are GT Deuce and then all bets are off). To put it in perspective about 90% of my roster plays every game. No place to hide bad recruiting there.
Hope that helps a little bit.
Namaste.